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• W2314621752 startingPage "10342" @default.
• W2314621752 abstract "The performance of the paradynamics (PD) reference potential approach in QM/MM calculations is examined. It is also clarified that, in contrast to some possible misunderstandings, this approach provides a rigorous strategy for QM/MM free energy calculations. In particular, the PD approach provides a gradual and controlled way of improving the evaluation of the free energy perturbation associated with moving from the EVB reference potential to the target QM/MM surface. This is achieved by moving from the linear response approximation to the full free energy perturbation approach in evaluating the free energy changes. We also present a systematic way of improving the reference potential by using Gaussian-based correction potentials along a reaction coordinate. In parallel, we review other recent adaptations of the reference potential approach, emphasizing and demonstrating the advantage of using the EVB potential as a reference potential, relative to semiempirical QM/MM molecular orbital potentials. We also compare the PD results to those obtained by direct calculations of the potentials of the mean force (PMF). Additionally, we propose a way of accelerating the PMF calculations by using Gaussian-based negative potentials along the reaction coordinate (which are also used in the PD refinement). Finally, we discuss performance of the PD and the metadynamics approaches in ab initio QM/MM calculations and emphasize the advantage of using the PD approach." @default.
• W2314621752 created "2016-06-24" @default.
• W2314621752 creator A5058944140 @default.
• W2314621752 creator A5088665303 @default.
• W2314621752 date "2012-08-21" @default.
• W2314621752 modified "2023-09-25" @default.
• W2314621752 title "Exploring, Refining, and Validating the Paradynamics QM/MM Sampling" @default.
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• W2314621752 doi "https://doi.org/10.1021/jp304678d" @default.
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• W2314621752 hasPublicationYear "2012" @default.
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